Package evaluation of VCFTools on Julia 1.13.0-DEV.1244 (c841b5fe7d*) started at 2025-10-02T21:45:04.978 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.73s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed CommonSolve ───────────── v0.2.4 Installed MacroTools ────────────── v0.5.16 Installed DelimitedFiles ────────── v1.9.1 Installed FillArrays ────────────── v1.14.0 Installed DataStructures ────────── v0.19.1 Installed CodecZlib ─────────────── v0.7.8 Installed HypergeometricFunctions ─ v0.3.28 Installed ConstructionBase ──────── v1.6.0 Installed AliasTables ───────────── v1.1.3 Installed TranscodingStreams ────── v0.11.3 Installed StatsBase ─────────────── v0.34.6 Installed SIMD ──────────────────── v3.7.1 Installed OrderedCollections ────── v1.8.1 Installed Combinatorics ─────────── v1.0.3 Installed VCFTools ──────────────── v0.2.10 Installed Statistics ────────────── v1.11.1 Installed DataAPI ───────────────── v1.16.0 Installed HypothesisTests ───────── v0.11.5 Installed ProgressMeter ─────────── v1.11.0 Installed QuadGK ────────────────── v2.11.2 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed IrrationalConstants ───── v0.2.4 Installed StatsAPI ──────────────── v1.7.1 Installed PrecompileTools ───────── v1.3.3 Installed LogExpFunctions ───────── v0.3.29 Installed Distributions ─────────── v0.25.120 Installed BufferedStreams ───────── v1.2.2 Installed Rmath ─────────────────── v0.8.0 Installed PtrArrays ─────────────── v1.3.0 Installed StatsFuns ─────────────── v1.5.0 Installed Roots ─────────────────── v2.2.10 Installed BioGenerics ───────────── v0.1.5 Installed InverseFunctions ──────── v0.1.17 Installed Reexport ──────────────── v1.2.2 Installed JLLWrappers ───────────── v1.7.1 Installed SpecialFunctions ──────── v2.5.1 Installed Preferences ───────────── v1.5.0 Installed Automa ────────────────── v1.1.0 Installed Missings ──────────────── v1.2.0 Installed PDMats ────────────────── v0.11.35 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installed Accessors ─────────────── v0.1.42 Installed BGZFStreams ───────────── v0.3.2 Installed VariantCallFormat ─────── v0.5.7 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.13/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.13/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.1 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.14.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.1 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.7 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 Installation completed after 8.77s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4346.7 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 377.43s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_PUTMpV/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.6 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.7 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_PUTMpV/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [38540f10] CommonSolve v0.2.4 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.0 [864edb3b] DataStructures v0.19.1 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.14.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.0.11 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.6 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.7 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.16.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.67.1+0 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 8.2s Test Summary: | Pass Total Time openvcf | 4 4 2.6s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.4s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.4s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 0%| | ETA: 0:32:49 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 14.505544 seconds (10.78 M allocations: 675.778 MiB, 5.43% gc time, 92.53% compilation time: 20% of which was recompilation) 0.439652 seconds (2.87 M allocations: 195.746 MiB, 8.40% gc time, 20.21% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:26:05 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.705538 seconds (4.57 M allocations: 310.202 MiB, 2.34% gc time, 85.40% compilation time) 0.412206 seconds (2.85 M allocations: 195.301 MiB, 5.84% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 21.6s Test Summary: | Pass Total Time get sampleID | 4 4 0.1s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 1.7s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.1s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 6.2s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:38 Progress: 0%|▏ | ETA: 0:18:40 Progress: 0%|▏ | ETA: 0:18:23 Progress: 0%|▏ | ETA: 0:18:05 Progress: 0%|▎ | ETA: 0:17:50 Progress: 1%|▎ | ETA: 0:17:45 Progress: 1%|▎ | ETA: 0:17:43 Progress: 1%|▎ | ETA: 0:17:43 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0:15:23 Progress: 10%|████▏ | ETA: 0:15:22 Progress: 10%|████▎ | ETA: 0:15:22 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:54:50 Progress: 20%|████████ | ETA: 0:07:20 Progress: 40%|████████████████▌ | ETA: 0:02:40 Progress: 62%|█████████████████████████▎ | ETA: 0:01:08 Progress: 84%|██████████████████████████████████▋ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 0 records are matched 227.099603 seconds (2.19 G allocations: 143.725 GiB, 6.30% gc time, 0.35% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m35.2s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:57:38 Progress: 19%|████████ | ETA: 0:07:25 Progress: 39%|████████████████▏ | ETA: 0:02:47 Progress: 61%|█████████████████████████ | ETA: 0:01:10 Progress: 84%|██████████████████████████████████▎ | ETA: 0:00:22 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 833 records are matched 121.214705 seconds (1.11 G allocations: 72.816 GiB, 6.15% gc time, 0.45% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:45:09 Progress: 20%|████████▏ | ETA: 0:07:10 Progress: 40%|████████████████▌ | ETA: 0:02:38 Progress: 62%|█████████████████████████▍ | ETA: 0:01:06 Progress: 85%|██████████████████████████████████▊ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 493 records are matched 119.764657 seconds (1.11 G allocations: 72.816 GiB, 6.14% gc time, 0.50% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:00:52 Progress: 20%|████████▎ | ETA: 0:06:47 Progress: 40%|████████████████▋ | ETA: 0:02:32 Progress: 61%|████████████████████████▉ | ETA: 0:01:07 Progress: 84%|██████████████████████████████████▍ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 0 records are matched 115.745410 seconds (1.11 G allocations: 72.816 GiB, 6.24% gc time, 0.50% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m59.0s 1.126372 seconds (1.29 M allocations: 91.617 MiB, 4.62% gc time, 84.05% compilation time) 0.975617 seconds (1.19 M allocations: 87.877 MiB, 3.38% gc time, 74.68% compilation time) 0.884540 seconds (1.19 M allocations: 86.889 MiB, 1.79% gc time, 79.38% compilation time) 0.308671 seconds (211.14 k allocations: 11.866 MiB, 99.94% compilation time) 0.007987 seconds (6.28 k allocations: 485.602 KiB, 96.11% compilation time) 0.008454 seconds (2.65 k allocations: 247.695 KiB, 96.40% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 7.9s 0.884046 seconds (977.00 k allocations: 75.632 MiB, 3.46% gc time, 76.79% compilation time) 0.812987 seconds (876.49 k allocations: 72.276 MiB, 2.44% gc time, 75.56% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.8s Test Summary: | Pass Total Time convert_ds | 5 5 0.9s 0.115523 seconds (525.34 k allocations: 50.449 MiB, 15.09% gc time, 26.42% compilation time) 0.580349 seconds (650.70 k allocations: 57.857 MiB, 2.23% gc time, 85.70% compilation time) ┌ Warning: Reached end of reader; columns 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:72 ┌ Warning: Reached end of reader; rows 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:176 0.071853 seconds (520.43 k allocations: 51.916 MiB, 13.29% gc time) 0.466506 seconds (593.98 k allocations: 56.208 MiB, 2.27% gc time, 83.86% compilation time) ┌ Warning: Reached end of record! Columns 1357-1400 are filled with 0.0s and are NOT haplotypes! └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:414 ┌ Warning: Reached end of record! Rows 1357-1400 are filled with 0.0s and are NOT haplotypes! └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:501 0.580806 seconds (1.56 M allocations: 81.843 MiB, 79.72% gc time, 2.92% compilation time: <1% of which was recompilation) 0.583458 seconds (1.70 M allocations: 90.492 MiB, 70.28% compilation time) ┌ Warning: Reached end of reader; columns 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:672 ┌ Warning: Reached end of reader; rows 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:787 Test Summary: | Pass Total Time convert to transpose functions | 13 13 6.4s Test Summary: | Pass Total Time record info | 14 14 4.5s Test Summary: | Pass Total Time write VCF | 3 3 3.7s 2.022709 seconds (5.30 M allocations: 381.114 MiB, 3.70% gc time, 53.64% compilation time) 0.947817 seconds (2.86 M allocations: 194.733 MiB, 4.03% gc time, 20.41% compilation time) 0.924438 seconds (4.89 M allocations: 358.376 MiB, 5.79% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 6.5s 0.881494 seconds (609.33 k allocations: 53.839 MiB, 1.67% gc time, 42.24% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.4s Test Summary: | Pass Total Time filter_chr | 4 4 1.4s Progress: 0%|▏ | ETA: 0:21:28 Progress: 1%|▍ | ETA: 0:20:14 Progress: 1%|▌ | ETA: 0:20:08 Progress: 2%|▋ | ETA: 0:20:01 Progress: 2%|▉ | ETA: 0:19:53 Progress: 2%|█ | ETA: 0:19:53 Progress: 3%|█▏ | ETA: 0:19:49 Progress: 3%|█▍ | ETA: 0:19:46 Progress: 4%|█▌ | ETA: 0:19:37 Progress: 4%|█▊ | ETA: 0:19:34 Progress: 5%|█▉ | ETA: 0:19:28 Progress: 5%|██ | ETA: 0:19:27 Progress: 5%|██▎ | ETA: 0:19:22 Progress: 6%|██▍ | ETA: 0:19:17 Progress: 6%|██▌ | ETA: 0:19:12 Progress: 7%|██▊ | ETA: 0:19:04 Progress: 7%|██▉ | ETA: 0:19:02 Progress: 7%|███ | ETA: 0:18:58 Progress: 8%|███▎ | ETA: 0:18:55 Progress: 8%|███▍ | ETA: 0:18:47 Progress: 9%|███▋ | ETA: 0:18:42 Progress: 9%|███▊ | ETA: 0:18:38 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A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 433 running 1 of 1 signal (10): User defined signal 1 jl_f_memoryrefnew at /source/src/builtins.c:1809 _deepcopy_memory_t at ./deepcopy.jl:116 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/DDn3I/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x738b99525426) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.13/Test/src/Test.jl:1952 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_invoke at /source/src/gf.c:4123 jl_toplevel_eval_flex at /source/src/toplevel.c:731 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2918 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:2978 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x738bbf502892) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2918 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:2978 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_68849.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:577 jfptr__start_63290.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x738bc0e62249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== Progress: 87%|███████████████████████████████████▋ | ETA: 0:02:40┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000738ba6ffc010 Total snapshots: 619. Utilization: 100% ╎617 @Base/client.jl:577 _start() ╎ 617 @Base/client.jl:310 exec_options(opts::Base.JLOptions) ╎ 617 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 617 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 617 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 617 @Base/loading.jl:2978 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 617 @Base/loading.jl:2918 include_string(mapexpr::typeof(identity), m… ╎ ╎ 617 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 617 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 617 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 617 @Base/loading.jl:2978 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 617 @Base/loading.jl:2918 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 617 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 617 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 617 @Test/src/Test.jl:1952 macro expansion ╎ ╎ ╎ 617 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 617 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 1╎ ╎ ╎ ╎ 98 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… 1╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:0 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 10 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 10 @VCFTools/…ts.jl:122 gtstats 1╎ ╎ ╎ ╎ 6 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ators.jl:424 > 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 3 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:964 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:385 checkbounds ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:381 checkbounds ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:11 length 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:10 size 2╎ ╎ ╎ ╎ ╎ 2 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:3186 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:954 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:941 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:146 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @VCFTools/…s.jl:169 hwe(n00::Int64, n01::Int64, n1… ╎ ╎ ╎ ╎ ╎ 1 @Distributions/…:102 ccdf ╎ ╎ ╎ ╎ ╎ 1 @Distributions/…:649 ccdf ╎ ╎ ╎ ╎ ╎ 1 @StatsFuns/….jl:9 chisqccdf ╎ ╎ ╎ ╎ ╎ 1 @StatsFuns/…jl:50 gammaccdf ╎ ╎ ╎ ╎ ╎ ╎ 1 @StatsFuns/…jl:48 gammaccdf ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:855 gamma_inc ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:855 gamma_inc ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:931 _gamma_inc(a::Floa… ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:13 erfc 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:15 _erfc ╎ ╎ ╎ ╎ 75 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 75 @Base/array.jl:2490 findfirst ╎ ╎ ╎ ╎ 73 @Base/array.jl:2439 findnext 11╎ ╎ ╎ ╎ ╎ 11 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 62 @Base/…ators.jl:1202 Fix ╎ ╎ ╎ ╎ ╎ 62 @Base/…tors.jl:1202 #_#59 ╎ ╎ ╎ ╎ ╎ 62 @Base/…tors.jl:178 isequal 62╎ ╎ ╎ ╎ ╎ 62 @Base/…ring.jl:187 == ╎ ╎ ╎ ╎ 2 @Base/array.jl:2440 findnext 2╎ ╎ ╎ ╎ ╎ 2 @Base/…otion.jl:637 == ╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:613 findgenokey 1╎ ╎ ╎ ╎ 1 @Base/…piler.jl:57 getproperty ╎ ╎ ╎ ╎ 2 @Base/array.jl:2490 findfirst ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:2439 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:673 isequaldata 1╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:78 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:964 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex 1╎ ╎ ╎ ╎ 1 @VCFTools/…rt.jl:225 geno_ismissing ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:82 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/array.jl:3186 getindex ╎ ╎ ╎ ╎ 1 @Base/range.jl:953 _getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:85 aim_select(record::VariantCallFo… 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:965 getindex 1╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:87 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 519 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 519 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 87 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 87 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 87 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:147 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:43 ensure_margin! ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:94 shiftdata!(stream::Buffer… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:291 copyto! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:294 _copyto_impl! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ion.jl:637 == ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:100 shiftdata!(stream::Buffe… 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:156 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:2115 empty! ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1278 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:211 _unsetindex! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:596 memoryref ╎ ╎ ╎ ╎ ╎ 55 @VariantCallFormat/…:165 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 50 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 11 @Base/array.jl:436 getindex 11╎ ╎ ╎ ╎ ╎ 11 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 36 @Base/array.jl:1335 push! ╎ ╎ ╎ ╎ ╎ 36 @Base/…ray.jl:1338 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1197 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1201 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + 2╎ ╎ ╎ ╎ ╎ ╎ 34 @Base/…ray.jl:1206 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1158 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1159 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1169 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:341 div ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1180 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1090 overallocation 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/…ay.jl:1181 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/…ay.jl:1101 array_new_memory 22╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/…ot.jl:588 GenericMemory 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ay.jl:1190 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:964 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:381 checkbounds 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…dvec.jl:481 all ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…dvec.jl:476 reduce ╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:832 reduce_and 2╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:847 macro expansion ╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:583 macro expansion ╎ ╎ ╎ ╎ ╎ 3 @Automa/…ry.jl:56 getindex 2╎ ╎ ╎ ╎ ╎ 3 @Automa/…ry.jl:49 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= ╎ ╎ ╎ ╎ ╎ 28 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 28 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 28 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 28 @BufferedStreams/…:5 readbytes! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/io.jl:0 readbytes!(s::TranscodingStream… ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/io.jl:1167 readbytes!(s::TranscodingStr… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:209 eof 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:212 eof ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @CodecZlib/…:195 process(codec::GzipDec… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:686 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ng.jl:402 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ng.jl:341 current_logger_for_en… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ng.jl:567 env_override_minleve… ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/io.jl:1168 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 9 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/io.jl:366 peek ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:298 peek ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:208 eof 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 3╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:209 eof ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:302 peek ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:964 getindex 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:385 checkbounds 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ls.jl:965 getindex ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/io.jl:1174 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ray.jl:400 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ay.jl:1020 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1024 _setindex! 9╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ay.jl:1025 _setindex! ╎ ╎ ╎ ╎ 432 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 432 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:384 copy 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 431 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 431 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 431 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 5╎ ╎ ╎ ╎ ╎ 431 @Base/…copy.jl:104 deepcopy_internal 2╎ ╎ ╎ ╎ ╎ 2 @Base/…copy.jl:0 _deepcopy_memory_t(x::Memory,… ╎ ╎ ╎ ╎ ╎ 2 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:113 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:594 memoryref 56╎ ╎ ╎ ╎ ╎ 56 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 12╎ ╎ ╎ ╎ ╎ 12 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 9╎ ╎ ╎ ╎ ╎ 9 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 23╎ ╎ ╎ ╎ ╎ 299 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:0 deepcopy_internal(x::Vector{U… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:128 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ct.jl:182 in 28╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:93 get ╎ ╎ ╎ ╎ ╎ ╎ 41 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:661 Array 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:649 Array ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ict.jl:81 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:88 * 34╎ ╎ ╎ ╎ ╎ ╎ 35 @Base/…ict.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ict.jl:87 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…lue.jl:59 getindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 201 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…ct.jl:182 in 62╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 135 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:182 in 24╎ ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:92 get 10╎ ╎ ╎ ╎ ╎ ╎ 111 @Base/…py.jl:104 deepcopy_internal 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 18╎ ╎ ╎ ╎ ╎ ╎ 93 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 15 @Base/…ry.jl:172 copy(a::Memory{UnitRange… 15╎ ╎ ╎ ╎ ╎ ╎ ╎ 15 @Base/…ot.jl:588 GenericMemory 1╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/…ry.jl:173 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ry.jl:136 unsafe_copyto! 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ry.jl:118 unsafe_copyto! 7╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…em.jl:28 memmove 46╎ ╎ ╎ ╎ ╎ ╎ 48 @Base/…ct.jl:86 setindex! 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ct.jl:87 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ue.jl:59 getindex 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:137 deepcopy_internal(x::Memory… 36╎ ╎ ╎ ╎ ╎ 36 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 9╎ ╎ ╎ ╎ ╎ 9 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1217 wait_forever at ./task.jl:1139 jfptr_wait_forever_30982.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] start_task at /source/src/task.c:1281 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000074afc2732b30 Total snapshots: 432. Utilization: 0% ╎432 @Base/task.jl:1139 wait_forever() 431╎ 432 @Base/task.jl:1217 wait() [433] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 jl_table_assign_bp at /source/src/iddict.c:57 [inlined] ijl_eqtable_put at /source/src/iddict.c:146 setindex! at ./iddict.jl:86 [inlined] _deepcopy_memory_t at ./deepcopy.jl:109 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_invoke at /source/src/gf.c:4123 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x738bbf5c0cb6) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _deepcopy_memory_t at ./deepcopy.jl:120 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/DDn3I/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x738b99525426) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.13/Test/src/Test.jl:1952 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_invoke at /source/src/gf.c:4123 jl_toplevel_eval_flex at /source/src/toplevel.c:731 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2918 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:2978 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x738bbf502892) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2918 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:2978 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1217 wait_forever at ./task.jl:1139 jfptr_wait_forever_30982.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] start_task at /source/src/task.c:1281 unknown function (ip: (nil)) at (unknown file) Allocations: 25694540 (Pool: 25693859; Big: 681); GC: 23 jfptr_IncludeInto_68849.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:577 jfptr__start_63290.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x738bc0e62249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) Allocations: 19254114067 (Pool: 19254098557; Big: 15510); GC: 33595 PkgEval terminated after 2721.71s: test duration exceeded the time limit